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Background  Integration of heterogeneous genes is widely applied in synthetic biology and metabolic engineering. However, knowledge about the effect of integrative position on gene expression remains limited.    Results  We established a genome-wide landscape of position effect on gene expression in  Saccharomyces cerevisiae . The expression cassette of red fluorescence protein (RFP) gene was constructed and inserted at 1044 loci, which were scattered uniformly in the yeast genome. Due to the different integrative loci on the genome, the maximum relative intensity of RFP is more than 13-fold over the minimum. Plots of the number of strains to RFP relative intensity showed normal distribution, indicating significant position effect on gene expression in yeast. Furthermore, changing the promoters or reporter genes, as well as carbon sources, revealed little consequences on reporter gene expression, indicating chromosomal location is the major determinant of reporter gene expression.    Conclusions  We have examined the position effects to integration genes expression in large number loci around whole genome in  S. cerevisiae . The results could guide the design of integration loci for exogenous genes and pathways to maximize their expression in metabolic engineering.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-017-0872-3) contains supplementary material, which is available to authorized users.

Genome-wide landscape of position effects on heterogeneous gene expression in Saccharomyces cerevisiae